JAL-2480 SequenceFeaturesI encapsulates features api

[jalview.git] / src / jalview / datamodel / features / SequenceFeaturesI.java

diff --git a/src/jalview/datamodel/features/SequenceFeaturesI.java b/src/jalview/datamodel/features/SequenceFeaturesI.java
new file mode 100644 (file)
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+++ b/src/jalview/datamodel/features/SequenceFeaturesI.java
@@ -0,0 +1,125 @@
+package jalview.datamodel.features;
+
+import jalview.datamodel.SequenceFeature;
+
+import java.util.List;
+import java.util.Set;
+
+public interface SequenceFeaturesI
+{
+
+  /**
+   * Adds one sequence feature to the store, and returns true, unless the
+   * feature is already contained in the store, in which case this method
+   * returns false. Containment is determined by SequenceFeature.equals()
+   * comparison.
+   * 
+   * @param sf
+   */
+  public abstract boolean add(SequenceFeature sf);
+
+  /**
+   * Returns a (possibly empty) list of features, optionally restricted to
+   * specified types, which overlap the given (inclusive) sequence position
+   * range
+   * 
+   * @param from
+   * @param to
+   * @param type
+   * @return
+   */
+  public abstract List<SequenceFeature> findFeatures(int from, int to,
+          String... type);
+
+  /**
+   * Answers a list of all features stored, optionally restricted to specified
+   * types, in no particular guaranteed order
+   * 
+   * @param type
+   * @return
+   */
+  public abstract List<SequenceFeature> getAllFeatures(String... type);
+
+  public abstract int getFeatureCount(boolean positional, String... type);
+
+  /**
+   * Answers a list of all positional features, optionally restricted to
+   * specified types, in no particular guaranteed order
+   * 
+   * @param type
+   * @return
+   */
+  public abstract List<SequenceFeature> getPositionalFeatures(
+          String... type);
+
+  /**
+   * Answers a list of all contact features, optionally restricted to specified
+   * types, in no particular guaranteed order
+   * 
+   * @return
+   */
+  public abstract List<SequenceFeature> getContactFeatures(String... type);
+
+  /**
+   * Answers a list of all non-positional features, optionally restricted to
+   * specified types, in no particular guaranteed order
+   * 
+   * @param type
+   *          if no type is specified, all are returned
+   * @return
+   */
+  public abstract List<SequenceFeature> getNonPositionalFeatures(
+          String... type);
+
+  /**
+   * Deletes the given feature from the store, returning true if it was found
+   * (and deleted), else false. This method makes no assumption that the feature
+   * is in the 'expected' place in the store, in case it has been modified since
+   * it was added.
+   * 
+   * @param sf
+   */
+  public abstract boolean delete(SequenceFeature sf);
+
+  /**
+   * Answers true if this store contains at least one feature, else false
+   * 
+   * @return
+   */
+  public abstract boolean hasFeatures();
+
+  /**
+   * Returns a set of the distinct feature groups present in the collection. The
+   * set may include null. The boolean parameter determines whether the groups
+   * for positional or for non-positional features are returned. The optional
+   * type parameter may be used to restrict to groups for specified feature
+   * types.
+   * 
+   * @param positionalFeatures
+   * @param type
+   * @return
+   */
+  public abstract Set<String> getFeatureGroups(boolean positionalFeatures,
+          String... type);
+
+  /**
+   * Answers the set of distinct feature types for which there is at least one
+   * feature with one of the given feature group(s). The boolean parameter
+   * determines whether the groups for positional or for non-positional features
+   * are returned.
+   * 
+   * @param positionalFeatures
+   * @param groups
+   * @return
+   */
+  public abstract Set<String> getFeatureTypesForGroups(
+          boolean positionalFeatures, String... groups);
+
+  /**
+   * Answers an immutable set of the distinct feature types for which a feature
+   * is stored
+   * @return
+   */
+  public abstract Set<String> getFeatureTypes();
+
+}
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